wheat: wheat dataset

Description

Information from a collection of 599 historical CIMMYT wheat lines. The wheat data set is from
CIMMYT's Global Wheat Program. Historically, this program has conducted numerous international
trials across a wide variety of wheat-producing environments. The environments represented in
these trials were grouped into four basic target sets of environments comprising four
main agroclimatic regions previously defined and widely used by CIMMYT's Global Wheat Breeding Program.
The phenotypic trait considered here was the average grain yield (GY) of the 599 wheat lines evaluated
in each of these four mega-environments.

A pedigree tracing back many generations was available, and the Browse application of
the International Crop Information System (ICIS), as described in
http://cropwiki.irri.org/icis/index.php/TDM_GMS_Browse (McLaren et al. 2005), was used
for deriving the relationship matrix A among the 599 lines; it accounts for selection and inbreeding.

Wheat lines were recently genotyped using 1447 Diversity Array Technology (DArT) generated by
Triticarte Pty. Ltd. (Canberra, Australia; http://www.triticarte.com.au). The DArT markers
may take on two values, denoted by their presence or absence. Markers with a minor allele frequency
lower than 0.05 were removed, and missing genotypes were imputed with samples from the marginal
distribution of marker genotypes, that is, x_{ij}=Bernoulli(\hat p_j), where \hat p_j
is the estimated allele frequency computed from the non-missing genotypes. The number of DArT
MMs after edition was 1279.

Usage

1

Format

Matrix Y contains the average grain yield, column 1: Grain yield for environment 1 and so on. The matrix A contains additive relationship
computed from the pedigree and matrix X contains the markers information.